Hi
Thanks for your help! However, I was mistaken - these reads are mulitplexed paired-end fastq files, and do not seem to be compatible with a Fastq Manifest import. I'm considering trimming in Qiime 1 (per How to demultiplex fastq file that still includes Barcodes and LinkerPrimer? - #3 by Nicholas_Bokulich) but that seems to leave me in the same position I'm in now. (Data structure will be difficult to deal with, and it does not seem that qiime1 has a Fastq manifest function?)
SO: I altered my data structure, renamed all files, concatenated, and renamed file type so that the data matched the EMP protocol. The issue I'm having now is that when I try to import, I get the following error:
There was a problem importing SD_Lane1: SD_Lane1/barcodes.fastq.gz is not a(n) FastqGzFormat file: Header on line 5 is not FASTQ, records may be misaligned
I've checked the header and this is what I have:
SampleID BarcodeSequence LinkerPrimerSequence
BM1Na CGTGAT caagcagaagacggcatacgagat
BM1Fa ACATCG caagcagaagacggcatacgagat
BM2Na GCCTAA caagcagaagacggcatacgagat
BM2Fa TGGTCA caagcagaagacggcatacgagat
BM3Na CACTGT caagcagaagacggcatacgagat
BM3Fa ATTGGC caagcagaagacggcatacgagat
BM4Na GATCTG caagcagaagacggcatacgagat
BM4Fa TCAAGT caagcagaagacggcatacgagat
BM6Na CTGATC caagcagaagacggcatacgagat
Any thoughts? Should I add more info to my barcodes file?
Thank you
Laura